EST information relating to tissue types in EMBL

Keith Bradnam keith at thale.life.nottingham.ac.uk
Tue Aug 15 05:47:27 EST 2000


Hello,

In response to a recent query, I've put together some figures regarding
the frequency of EMBL Arabidopsis EST sequences from different tissue
types.  As this info may be of interest to others, I thought I would post
it here.

There are nearly 110,000 Arabidopsis EST sequences in the EMBL database.
The majority of these have been released since the last full release of
EMBL (release 63) and are only available if you search EMBL's daily update
files.  The majority of these sequences have a 'tissue_type' qualifier
listed in their database annotation.  For the 79,163 EST sequences which
have this information, the tissue types are as follows:


Number of ESTs   Tissue type description
========================================
18,947           roots
15,767           above-ground organ
12,752           green siliques
10,738           seed
  5,827           flower buds
  2,351           rosette
  2,045           seedling hypocotyl
  1,647           whole seedlings of A. thaliana ecotype
  1,161           liquid-cultured seedlings
  1,084           cell suspension culture  of ecotype columbia
  1,059           inflorescence
  1,006           leaves, flowering plants
    990           Flower buds of A.thaliana ecotype columbia C24
    707           sliced leaves of A.thaliana ecotype columbia
    678           Green siliques of A.thaliana ecotype columbia
    642           leaves, seedlings
    346           Dry seeds of A.thaliana ecotype columbia
    333           seedlings, leaf and root
    325           green shoots of A.thaliana ecotype columbia
    241           roots of nitrate treated liquid-cultured A.thaliana
    201           inflorescence with predominately younger flower buds
    105           Flowering tips of ecotype Landsberg erecta
     60           cell suspension culture of A.thaliana
     49           whole plant
     27           Excised pieces of roots containing nematode feeding sites
     20           inflorescence apex with young flowers (<~Stage 9)
     17           Above-ground organ from two to six-week old plants
     16           Germinating seeds
      6           7 day old germinated etiolated seeds
      3           immature siliques
      1           shoots


Please note that these tissue-type descriptions are listed exactly as they
appear in the EMBL record.  So presumably 'green siliques' and 'Green
siliques of A.thaliana ecotype columbia' reflect the same tissue, though
they are listed separately above.

Also note that of these 79,163 EST sequences, 62,569 are sequences that
have been released since the last full release of the EMBL database.

Given the speed at which new EST sequences are being released to EMBL it
is highly likely that by the time you read this, these figures will be out
of date!

This information will be made available as part of the Arabidopsis Genome
Resource (AGR).  For now, the information will be posted on the AGR web
page (http://ukcrop.net/agr/) and in due course the database will be
rebuilt to reflect this useful information and you will be able to search
EST sequences by tissue type.

Regards,

Keith

~  Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR)
~  Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/
~  University Park, University of Nottingham, NG7 2RD, UK
~  Tel: (0115) 951 3091






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